Yep, this opinion needed to be expressed. ME3 is my personal favorite, but I love the whole trilogy. I think the ending, with the Extended Cut, is ultimately satisfying, and encourages us to consider the consequences of all the world-changing decisions we made. I was frustrated with the original presentation, and the EC isn't perfect, but I greatly appreciate the intended point.
The story was about Shepard as a Nietzchean Übermensch, a charismatic soldier who managed to unite an entire galaxy and overthrow a billion-year-old evolutionary control system. He fought the gods themselves, and made a choice that transcended the domain of mortals, beyond good and evil; the choice of a god. He either killed them, replaced them, or reconciled them with the mortal realm. He was a champion of life, and was granted the authority to define it. He will be remembered for all time. The stuff of legends and myths.
Just trying to bring some positivity to this often pessimistic forum. 
I saw it a little differently to you but thats an interesting take. I've done no university level courses on Philosophy but I've read a few books by good authors and ME is my favourite game from a narrative perspective, especially ME1. Some notes below:
Summary
Modern reinvention of classic literature in the context/environment of Sci-Fi. A true masterpiece IMHO.
Protagonist (Shepard) - Classic Hero Archtype
- tension between meaning and absurdity—as the fundamental condition of human existence.
- identify the core concepts of "necessity," "fate," and "heroic excellence" as they define the Hero's life mission and task. Consider the notion of the agon - the struggle of the Hero to fulfill his or her destiny.
- Greek drama, and a further incarnation of the "Heroic ideal", the tragic hero. Contemplate Aristotle's and Nietzsche's seminal ideas on tragic drama, where beauty and transcendence arise from a willing embrace of life.
- Influences Plato's republic, the 'heroic ideal' late stoicism.
By every account, the Shepard is the classic hero, very well explored through the narrative.
Antagonist (Reapers) - an Epitome of philosophy on the absurdity and the meaning of life.
In my opinion, as beautiful as the protagonist is explored, the antagonist and its embodiment of philosophy ideas is even more of a masterpiece. Its less about the reapers as a thing/person, and more about what they represent.
The reapers are the logical advancement of human kind, tens of thousands to millions of years in the future. And its a reconsideration of the same philosophical ideas we have today, millions or perhaps a billion years in the future.
Underwritten in the rhetoric of 'The Great Filter', through 'The Fermi Paradox', (two sci-fi concepts), the reapers create an environment to consider their philosophical questions in one of the most intense ways I've ever seen it realized.
I could write 10 pages on why I think the antagonist is really interesting but I think its something you need to start pulling threads on and see it unwrap yourself.
Conclusion
So, although i some Nietzsche's ideas floating around, I dont really see the ubermensche. I see an classic hero, (perhaps in stark contrast to your opinion, it is that the hero could come from the common man), in battle with the reapers, (who are the embodiment of meaning and absurdity). This is played out on an amazing sci-fi landscape.
I know that the 'great filter' has been written about before. Either the guys behind this like Drew are complete geniuses or perhaps they borrowed and built it off some really great authors doing similar stuff in the past. Either way, my favourite game in terms of narrative by far 
Gameplay in 2-3 were the best, and they were great games. However, narrative in ME1 was was superior IMHO, a home run.
After finishing ME1, all the excellence in narrative and literature was underpinned and complete. Playing games 2-3 was really just a formality and essentially just controlling the hero as he finished off the story. Even though the character development was arguably better in 2-3, from a strictly narrative perspective, ME1 wins for me hands down, because its where all the main themes/ideas happens. After you finish ME1, all the cool concepts that I mentioned above are already explored, all that is left is playing out the rest of the trilogy to win with a bunch of interesting but smaller ideas/concepts being explored.
This said, I would play 10 more ME games because the intrigue, exploration, and various other subplots alone were excellent and superior to most other games so they've a fan in me for life now.